7-5308283-G-A
Variant names:
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_001080495.3(TNRC18):c.8730C>T(p.Asp2910Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 1,611,854 control chromosomes in the GnomAD database, including 22,717 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.14 ( 1641 hom., cov: 33)
Exomes 𝑓: 0.17 ( 21076 hom. )
Consequence
TNRC18
NM_001080495.3 synonymous
NM_001080495.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.44
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BP6
Variant 7-5308283-G-A is Benign according to our data. Variant chr7-5308283-G-A is described in ClinVar as [Benign]. Clinvar id is 1250212.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.44 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TNRC18 | ENST00000430969.6 | c.8730C>T | p.Asp2910Asp | synonymous_variant | Exon 30 of 30 | 5 | NM_001080495.3 | ENSP00000395538.1 | ||
TNRC18 | ENST00000399537.8 | c.8730C>T | p.Asp2910Asp | synonymous_variant | Exon 30 of 30 | 5 | ENSP00000382452.4 |
Frequencies
GnomAD3 genomes AF: 0.137 AC: 20858AN: 152114Hom.: 1641 Cov.: 33
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GnomAD3 exomes AF: 0.149 AC: 36288AN: 244034Hom.: 2928 AF XY: 0.148 AC XY: 19694AN XY: 132694
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GnomAD4 exome AF: 0.166 AC: 242268AN: 1459622Hom.: 21076 Cov.: 35 AF XY: 0.164 AC XY: 118844AN XY: 725928
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GnomAD4 genome AF: 0.137 AC: 20853AN: 152232Hom.: 1641 Cov.: 33 AF XY: 0.139 AC XY: 10349AN XY: 74418
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
May 05, 2021
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at